tbuckley/cabot-search huggingface dataset:
Abstract 1906: MSH3: An underestimated DNA MMR gene in colorectal carcinogenesis and its potential role in disparity
Authors: Mudasir Rashid, Rumaisa Rashid, Minoru Koi, John M. Carethers, Hassan Brim, Hassan Ashktorab
Journal: Cancer Research (2023)

Abstract Background: Unique mutations in cancer genes have been found in different races including African Americans (AA) population. Maintenance of proficient mismatch repair genes is important in colorectal cancer. Among them, MSH3 is found to be more important in colorectal cancer in AA particularly as its alterations associate with EMAST phenotype that has poor prognosis. However, there are regional variations in the classification and criteria used to determine the pathogenicity of these mutations particularly in AA due to their high genomic diversity. Aim: To analyze unique and novel MSH3 mutations using specific in-silico prediction tools and to validate their biological significances in AA-CRC. Results: In this study, we validated our targeted exome sequencing data of MSH3 mutations in AA and Caucasians (CA) CRC samples. A cost effective in-silico approach was employed to narrow down most significant MSH3 mutations. Interestingly, we and found six non-synonymous novel, pathogenic mutations in MSH3 gene (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) correspond to MSH3 protein (E413K; S466N; S920F; E976K; H1010Y; E1081K), in AA than CA samples. Also, we observed loss or gain of different chemical bonding patterns (hydrogen, ionic, hydrophobic, and di-sulfide bonding) between wild type and mutant MSH3 protein. Interestingly, some of these mutations were within the ATPase site while others are in MSH3-MSH2 interacting domains. Furthermore, Molecular Dynamics Simulation (MDS) of these six mutants of MSH3 proteins showed an overall effect on MSH3 protein stability especially in MSH3-MSH2 interaction compared to wild type MSH3 protein.Conclusion: Our data showed that, six MSH3 non-synonymous mutations are deleterious as they affect important sites within MSH3-MSH2 interactive and ATPase domain. Assessing the real frequency of these mutations in large cohort and their specific effect on function may shed light on EMAST phenotype, high prevalence, and overall poor prognosis in the AA population. In vitro functional assays using CRISPR-Cas9 knock-in and in vivo studies are underway to mimic these mutations. Citation Format: Mudasir Rashid, Rumaisa Rashid, Minoru Koi, John M. Carethers, Hassan Brim, Hassan Ashktorab. MSH3: An underestimated DNA MMR gene in colorectal carcinogenesis and its potential role in disparity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1906.
Abstract 336: Role of ST6GAL1 sialyltransferase in early stages of pancreatic cancer development
Authors: Susan L. Bellis, Asmi Chakraborty, Nikita Bhalerao, Michael Marciel, Jihye Hwang, Austin Silva
Journal: Cancer Research (2023)

Abstract Increased cell surface sialylation is a prevalent feature of tumor cells. The addition of sialic acid (a negatively-charged sugar) to select surface receptors modulates the structure and function of these receptors, leading to changes in intracellular signaling and gene expression. Increased tumor cell sialylation occurs, in part, through the upregulation of sialyltransferases such as ST6GAL1, an enzyme that adds an α2-6 linked sialic acid to N-glycosylated proteins. ST6GAL1 is overexpressed in numerous malignancies, including pancreatic ductal adenocarcinoma (PDAC), and high expression correlates with a poor prognosis. Our group has shown that ST6GAL1 plays a causal role in promoting PDAC initiation and progression in tumor xenograft and genetically-engineered mouse (GEM) models. As one example, we developed a GEM model with conditional ST6GAL1 expression in the pancreas and crossed this line to the “KC” PDAC model, which expresses oncogenic Kras (KrasG12D). Mice with dual expression of ST6GAL1 and KrasG12D (”KSC” mice) exhibit greatly accelerated PDAC initiation, progression, and mortality when compared with KC mice. In light of ST6GAL1's known role in conferring progenitor-like cell characteristics, we postulated that ST6GAL1 activity contributes to PDAC initiation by fostering acinar to ductal metaplasia (ADM). During ADM, pancreatic acinar cells de-differentiate into ductal-like, progenitor cells and acquire greater proliferative potential as well as apoptosis resistance. Cells undergoing ADM are particularly vulnerable to Kras-dependent transformation. Using a variety of approaches and model systems including GEM organoids, 3D acinar cultures, acinar-like cell lines, and an in vivo assay for ADM, we uncovered a novel function for ST6GAL1 in promoting ADM. We further determined that high ST6GAL1 activity in acinar cells cooperates with KrasG12D to drive neoplasia. Finally, our studies suggest that the tumor-promoting effects of ST6GAL1 are mediated, at least in part, by ST6GAL1-mediated sialylation of EGFR. These collective results highlight a novel glycosylation-dependent mechanism involved in early stages of PDAC development. Citation Format: Susan L. Bellis, Asmi Chakraborty, Nikita Bhalerao, Michael Marciel, Jihye Hwang, Austin Silva. Role of ST6GAL1 sialyltransferase in early stages of pancreatic cancer development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 336.
Abstract 2348: Mapping the interactome of matrisome targets using extracellular proximity labeling (ePL)
Authors: David Peeney, Sadeechya Gurung, Josh Rich, Sasha Coates-Park, Yueqin Liu, William G. Stetler-Stevenson
Journal: Cancer Research (2023)

Abstract Classical methods to investigate protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore PPIs in living systems. PL has distinct advantages over traditional protein interactome studies, such as the ability to identify weak and transient interactions in vitro and in vivo. Most PL studies are performed on targets within or on the cell membrane. We describe a method to investigate PPIs within the extracellular compartment, using both BioID2 and TurboID, that we term extracellular PL (ePL). To demonstrate the utility of this modified technique, we investigate the interactome of the widely expressed matrisome protein Tissue inhibitors of metalloproteinases 2 (TIMP2). Tissue inhibitors of metalloproteinases (TIMPs) are a family of multi-functional proteins that were initially defined by their ability to inhibit the enzymatic activity of matrix metalloproteinases (MMPs), the major mediators of ECM breakdown and turnover. TIMP2 is a unique family member, with a broad expression profile that is expressed in both normal and diseased tissues, even in those with minimal metalloproteinase activity. Understanding the functional transformation of matrisome regulators, like TIMP2, during the evolution of tissue microenvironments associated with disease progression is essential to the development of ECM targeted therapeutics. This knowledge may also garner understanding of therapeutic resistance and the failure of conventional and next-generation cancer therapies. Using carboxyl- and amino-terminal fusion peptides of TIMP2 with BioID2 and TurboID, we describe the TIMP2 interactome in unique tissue compartments. We also illustrate how the TIMP2 interactome changes in the presence of different stimuli, in different cell lines, and with different reaction kinetics (BioID2 vs. TurboID); demonstrating the power of this technique and comparing our findings with classical PPI methods. We propose that the screening of matrisome targets in disease models using ePL will reveal new therapeutic targets for further comprehensive studies. Citation Format: David Peeney, Sadeechya Gurung, Josh Rich, Sasha Coates-Park, Yueqin Liu, William G. Stetler-Stevenson. Mapping the interactome of matrisome targets using extracellular proximity labeling (ePL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2348.
Abstract 341: Critical role of defensins in respiratory viral infection induced breast cancer progression
Authors: Umer Ali, Venkataswarup Tiriveedhi
Journal: Cancer Research (2023)

Abstract Respiratory viral infections (RVI) such as influenza and COVID19 impact the host systemic immune system along with causing deleterious chronic inflammatory responses and respiratory distress. While the role of chronic inflammation in cancer is well-established, the role of RVI on tumorigenesis is poorly defined. To study the role of RVI on breast cancer, we first infected murine respiratory epithelial cells (mRES) with murine sendai virus (mSV), an analog for human parainfluenza virus. These infected mRES were co-cultured with 4T1 murine breast cancer cells in 1:1 dilution on a single 2D plate and also in trans-well format. Both in co-culture and transwell culture we saw a 40-80% (p&amp;lt;0.05) increased proliferation of breast cancer cells. Similarly, when 4T1 cells were treated with the supernatant collected from infected mRES cells in 1:5 dilution, also demonstrated a 2.3 fold increased breast cancer cell proliferation. The cytokine analysis from the supernatant collected from infected mRES cells demonstrated a 17-23 fold enhanced secretion of α/β-defensins. Direct treatment of α-defensin (cyptidin-4, 10 pg/mL) and β-defensin-3 (mBD3, 20 pg/mL) on 4T1 cells demonstrated enhanced expression of chemokine metastatic receptor, CXCR4 (4.3 fold), angiogenic factor, VEGF (12.8 fold) and cell division favoring factor, CDK2 (8.1 fold). Further, analysis of infected mRES cells demonstrated upregulation of toll-like receptor 2 (TLR2) and NOD-like receptor protein 3 (NLRP3) expression. Interesting, co-cultured of infected mRES with syngeneic murine CD4 T cells induced exhaustion phenotype (PD1+ and CTLA4+) differentiation of CD4 T cells. Taken together, these data suggest that respiratory viral infections through induction of cancer cell proliferation and inhibiting anti-tumor adaptive immune responses promote breast cancer proliferation. Citation Format: Umer Ali, Venkataswarup Tiriveedhi. Critical role of defensins in respiratory viral infection induced breast cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 341.
Abstract 2501: A glioblastoma and blood-brain barrier <i>in vitro</i> model to assess the tumor microenvironment and temozolomide resistance
Authors: Maxine S. Lam, Joey Aw, Damien Tan, Ragavi Vijayakumar, Khloe S. Gordon, Michael E. Birnbaum, Radoslaw M. Sobota, Giulia Adriani, Andrea Pavesi
Journal: Cancer Research (2023)

Abstract Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults with a dismal prognosis. Currently, Temozolomide (TMZ) and Bevacizumab are the main approved agents for primary and recurrent GBM, respectively. However, TMZ resistance is frequent and Bevacizumab does not improve overall survival. The heterogeneity of GBM and the presence of a highly selectively permeable blood-brain barrier (BBB) preclude the use of chemotherapeutics approved for other malignancies. Meanwhile, new therapy development is limited in part because most pre-clinical models do not recapitulate the key features of GBM that are relevant to therapy resistance and drug delivery. This is particularly important when validating immunotherapies such as engineered T cell therapy, which has shown some promise in the clinics. We therefore developed an in vitro 3D model that recapitulates the major features of the GBM tumor microenvironment (TME) that are involved in therapy resistance, including the dense tumor core and infiltrating invasive front observed in clinical tumors, surrounded by a perfusable BBB with a physiological permeability. With this model, we investigate the angiogenic nature of GBM, and the role of tumor organization and the TME in TMZ resistance and immunosuppression. We find that TMZ sensitivity decreases as complexity of tumor cell 3D organization increases, and identify pathways potentially associated with TMZ resistance and immunosuppression using proteomics and genomics approaches. Additionally, we find that tumor-associated vasculature has a higher permeability due to VEGFA from GBM tumors, which leads to the downregulation of endothelial junction proteins. Using an IL13Ra2-targetting chimeric antigen receptor (CAR) T cell as a model for engineered T cell therapy, we find that tumor-associated vasculature acts as a physical barrier to CAR-T cell extravasation, significantly impeding CAR-T cell efficacy. We then use the model to screen a CAR library to identify novel CAR combinations that can improve CAR-T cell extravasation and cytotoxicity in GBM. Citation Format: Maxine S. Lam, Joey Aw, Damien Tan, Ragavi Vijayakumar, Khloe S. Gordon, Michael E. Birnbaum, Radoslaw M. Sobota, Giulia Adriani, Andrea Pavesi. A glioblastoma and blood-brain barrier in vitro model to assess the tumor microenvironment and temozolomide resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2501.
Abstract 4322: AI assisted detection and characterization of tertiary lymphoid structures in patients with colorectal cancer
Authors: Samantha Burg, Nathaniel Hart, Astin Powers, Wenjun Zhang
Journal: Cancer Research (2023)

Abstract Tertiary Lymphoid Structures (TLSs) are ectopic immune cell aggregates that form in response to abnormal physiology and inflammation. TLS presence in the tumor environment has been associated with positive clinical outcomes and response to immune checkpoint inhibition therapy. Using a fluorescent multiplex panel consisting of Pan-cytokeratin (PanCK), Programmed Death Ligand-1 (PD-L1), cluster of differentiation (CD) 8, CD3, and CD68 we developed a HALO-based artificial intelligence (AI) classifier to detect TLSs in colorectal cancer (CRC) tissue. In conjunction with cell-type and spatial analyses, we used the AI TLS classifier to characterize several features of the TLS and peri-TLS environment. We trained the AI classifier using 51 examples of TLSs from 8 patients, and applied it to images of 21 CRC patient tissues. TLSs were detected in 9/21 patient samples. We then used cellular detection and spatial analysis to characterize features of the TLS, including the germinal center (GC), T cell zone and peri-TLS area. We detected a higher cell density (Mean=12250 ±2039 SD; cells/mm2) within the interior of AI-detected GCs relative to the 1st 200 μm outside of the AI-defined GC border (8005±1870). In addition, we examined the spatial distribution of CD3+ and CD8+ T cells relative to the TLS GC. We found elevated CD3+ cell density in the interior of the GC (5784±1649) and within 200 μm of the GC border (5126±2239) which decreased at distances &amp;gt;200 μm from the GC border. We found CD8+ density to be elevated within the 1st 200 μm of the GC border (1903±1182) and declined 400 μm away from the GC border (963±828). The spatial distribution of T cells surrounding an area of high cell density is indicative of a T cell zone surrounding germinal center. Further analysis of the AI-detected TLS GCs indicated that PD-L1+ cell density was highest within the germinal center (355± 534;9) relative to the exterior of the germinal center (1st 150μm outside germinal center:276± 441). We created an AI classifier that can detect TLS(s) within patient tissue in the absence of a B-cell marker and confirmed that our AI classifier was detecting TLSs by characterizing canonical features of TLSs. Further exploration of the TLS and peri-TLS area may offer insights into immune-tumor interaction within the tumor microenvironment, and paired detection of TLSs in a clinical cohort with outcome data may predict patient response to immune checkpoint inhibitor therapy. Citation Format: Samantha Burg, Nathaniel Hart, Astin Powers, Wenjun Zhang. AI assisted detection and characterization of tertiary lymphoid structures in patients with colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4322.
Abstract 1070: The anti-tumor efficacy of combining oral ATR kinase inhibitor ceralasertib with TIC10/ONC201, an oral Akt/ERK inhibitor, TRAIL pathway and integrated stress response inducer, in prostate cancer treatment
Authors: Yutong Xia, Maximilian P. Schwermann, Andrew George, Anna Ochsner, Benedito A. Carneiro, Wafik S. El-Deiry
Journal: Cancer Research (2023)

Abstract Prostate cancer is the most common cancer and the second leading cause of cancer death among men in the United States. There are 268,490 estimated new cases and 34,500 estimated deaths in 2022 according to the NIH. Patients with metastatic castration resistant prostate cancer (mCRPC) have a poor prognosis and the current treatment options show limited efficacy. From the TRAP trial, 20% of mCRPC patients are reported to bear DNA repair defects. Ceralasertib, formerly known as AZD6738, is a potent and selective orally bioavailable inhibitor of the ataxia tenlangiectasia and Rad3-related (ATR) kinase, which is involved in DNA repair in response to DNA damage and replication stress. Ceralasertib’s antitumor activity as a monotherapy in treating prostate cancer is moderate. Thus, we investigated a combination therapy of ceralasertib with ONC201, a potent and cytotoxic orally bioavailable inhibitor of the serine/threonine protein kinase Akt and extracellular signal-regulated kinase (ERK). Upon administration, ONC201 can induce tumor cell apoptosis mediated by tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and activate integrated stress response (IRS). Preliminary results demonstrate synergistic activity with the combination therapy in vitro using CellTiterGLO viability assay 72 hours in a 96 well plate post treatment. Ongoing studies using western blotting and cytokine profiling are intended to illustrate the mechanism behind the proven synergy. Our results aim to solve the overarching need in developing novel therapeutic strategies to overcome resistance in current prostate cancer treatments. Citation Format: Yutong Xia, Maximilian P. Schwermann, Andrew George, Anna Ochsner, Benedito A. Carneiro, Wafik S. El-Deiry. The anti-tumor efficacy of combining oral ATR kinase inhibitor ceralasertib with TIC10/ONC201, an oral Akt/ERK inhibitor, TRAIL pathway and integrated stress response inducer, in prostate cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1070.
Abstract 5009: Inhibition of TGFBR2 signaling re-sensitizes TMZ-resistant glioblastoma cells to therapy
Authors: Maya K. Johnson, Jack Korleski, Amanda Johnson, Sophie Sall, John Laterra, Hernando Lopez-Bertoni
Journal: Cancer Research (2023)

Abstract Glioblastoma (GBM), the most aggressive and lethal form of brain tumors, recurs in 90% of cases and the standard protocol of care—temozolomide (TMZ)—is an ineffective method to combat chemo-resistant GBM. It is therefore imperative that we identify, develop, and design novel therapeutics to effectively combat recurrent GBM (rGBM). Multi-potent stem-like cell subpopulations within GBM (also referred to as glioma stem cells or GSCs) play important roles in tumor propagation, therapeutic resistance, and recurrence following treatment. Understanding the molecular mechanisms that drive resistance in GSCs can lead to novel therapeutic approaches for rGBM. Bioinformatics analyses of transcriptome data sets from rGBM clinical specimens identified transforming growth factor-beta receptor type 2 (TGFBR2) as a putative driver of resistance and recurrence in GBM. We show that TMZ-resistant cells become more stem-like concurrent with higher expression of TGFBR2 protein and mRNA. Importantly, shRNA-mediated inhibition of TGFBR2 decreases proliferation of TMZ-resistant cells and enhances the effects of TMZ. We hypothesize that by developing targeted therapeutics to reduce TGFBR2 expression we will inhibit the growth capacity and/or re-sensitize rGBM cells to ionizing radiation (IR) or TMZ treatment by simultaneously targeting multiple putative oncogenes implicated in the induction of stem-like resistant GBM cell subsets. Future directions include inhibiting TGFBR2 signaling in clinical specimens derived from rGBM patients using two translatable approaches: (1) ITD1, a small molecule TGFBR2 inhibitor predicted to cross the blood-brain-barrier and (2) microRNAs to target multiple TGFBR2 target genes up-regulated in rGBM. Citation Format: Maya K. Johnson, Jack Korleski, Amanda Johnson, Sophie Sall, John Laterra, Hernando Lopez-Bertoni. Inhibition of TGFBR2 signaling re-sensitizes TMZ-resistant glioblastoma cells to therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5009.